Hello there,
To present brievly the plot, we're comparing consensus sequences at several base frequencies, generated by both illumina sequencing and long reads ONT. To do so, we've aligned our fastq on the reference (a linearized hepatitis B virus genome).
The next step is to use the samtools mpileup function on these bam, then evaluating base repartition on each position to generate consensus.
However we are a bit lost with the specific parameters to use for long read ONT and Illumina output. After consulting this mpileup doc, I guess we have to jungle with --min-BQ and --min-MQ parameters. However these options seems more adapted to Illumina data than ONT.
It is possible to correctly use them for ONT data? Do you have any recomandations/advices with the parameters to use for a balanced comparision?
Thank you for your time once again, help provided on these forums is truely appreciated:)
Hadrien
Hello Hadrien,
did you find the right way to do it? could you share your exprience please?
thank you